In March 2014, the International Court of Justice formally ruled that the ICR's whaling program was not for scientific purposes, as claimed, and ordered Japan to immediately cease its operation.

[11][12] In March 2014 the International Court of Justice (ICJ) ordered Japan to cease the JARPA II programme stating that its Antarctic whaling was in contravention of the IWC moratoria 10(e) and 10(d).

[citation needed] The ICR also claims to have conducted sighting surveys in the southern hemisphere and the north Pacific to elucidate trends in abundance, density, distribution, and behavior of whales.

In 1997 the IWC scientific committee reviewed the JARPA program and disagreed on whether the ICR's lethal methods were necessary, but it was concluded that the results could potentially allow for an increase in the number of minke whales killed.

In 2002, after completing its initial study, the ICR proposed a longer-term program in the Pacific within Japan's Exclusive Economic Zone.

The full program introduced a change from previous use of the ICRW Article VIII research provision by not specifying an end date.

"[23] In 2000, 2001 and 2003, more resolutions were passed by the IWC urging Japan to cease issuing special permits for whaling and limit research to non-lethal methods.

[28] In an open letter to the Japanese government, published in 2002 in the New York Times and sponsored by the World Wildlife Fund (WWF), 21 scientists declared that they "believe Japan's whale "research" program fails to meet minimum standards for credible science".

They were "concerned that Japan's whaling program is not designed to answer scientific questions relevant to the management of whales; that Japan refuses to make the information it collects available for independent review; and that its research program lacks a testable hypothesis or other performance indicators consistent with accepted scientific standards".

[32] In the same issue, twenty members of the Scientific Committee of the International Whaling Commission confirmed "that the signers of the open letter correctly summarized criticisms made by researchers very familiar with Japanese scientific whaling", a fact omitted by the letter's critics, "betraying a selectiveness that pervades their article".

According to them, "so little of any significance to IWC management can be obtained only from whaling catches that it is impossible to justify killing animals on this basis".

In 2008 the ICR was criticized by anti-whaling proponents when photographs released by the Australian government showed pictures of the ICR harpoon ship Yushin Maru killing several different whales, and a whale and her calf being taken on board the Nisshin Maru for processing[34] The Australian government used that opportunity to voice their disbelief of the ICR's scientific research claims:"The scientists who have considered carefully the material that has been put forward by Japanese scientists in the past, making some claim that their whaling is scientific, have found that it is without foundation.

"Animal rights groups such as Greenpeace[citation needed] and Sea Shepherd Conservation Society have repeatedly attacked the institute's vessels and personnel while carrying out their duties.

In 2010, an employee of the institute reportedly sustained chemical burns to his face from a butyric acid projectile launched by a member of the Sea Shepherd organisation.

[37] On March 31, 2014, the International Court of Justice ruled that Japan's whaling program was not for scientific purposes and forbade the granting of further permits.

[41][42] In November 2014, Japan announced that it would resume hunting whales in the Southern Ocean, but that it would reduce its catch target by two-thirds.

In January 2015, the Japanese Fisheries Agency announced that the ICR was launching a non-lethal whale research programme until March 28.

It then resumed commercial hunting in its territorial waters and exclusive economic zone on July 1, 2019, but ceased whaling activities in the Antarctic Ocean.